From Code to Crop: How Bioinformatics is Transforming Crop Genomics in Modern Agriculture and Bettering Environment
Prajval V, A. Krishnamoorthi, Riya Thakur, Ruchitha T, Manish Kapoor, Anushi, Abhishek Singh, Karthik Chittibomma
Journal of Advances in Biology & Biotechnology · pp. 27–49 · Published 16 Mar 2024
10.9734/jabb/2024/v27i4737Abstract
Advancements in bioinformatics have ushered in a new era in modern agriculture by seamlessly integrating computational methodologies with crop genomics. This paper explores the transformative impact of bioinformatics on crop genomics and its consequential benefits for both agriculture and the environment. Bioinformatics tools and techniques are instrumental in decoding the intricate genetic information of crops, leading to the development of tailored solutions for improved crop yield, resistance to diseases, and environmental sustainability. The first aspect of this transformation involves the utilization of high-throughput sequencing technologies, which generate vast amounts of genomic data. Bioinformatics algorithms play a crucial role in processing and analysing these data sets, enabling researchers to unravel the complex genetic codes of crops efficiently. This genomic information serves as a foundation for precision breeding programs, allowing scientists to identify desirable traits and accelerate the development of crops with enhanced resilience and productivity. Furthermore, bioinformatics facilitates the identification of molecular markers associated with key agronomic traits. This information enables the implementation of marker-assisted breeding, a technique that expedites the selection of desired traits in crops, reducing the time and resources required for traditional breeding methods. The result is the development of crop varieties that are not only more productive but also more resistant to pests and diseases, contributing to global food security. Beyond enhancing crop performance, bioinformatics-driven crop genomics also addresses environmental concerns. By deciphering the genetic basis of stress tolerance and resource- use efficiency, researchers can develop crops that require fewer inputs such as water, fertilizers, and pesticides. This not only benefits farmers economically but also reduces the ecological footprint of agriculture, promoting sustainable practices and minimizing environmental impact.
References (94)
- 1 Food Security: The Challenge of Feeding 9 Billion People [DOI]
- 2 PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences [DOI]
- 3 TASSEL: software for association mapping of complex traits in diverse samples [DOI]
- 4 Global food demand and the sustainable intensification of agriculture [DOI]
- 5 Phytozome: a comparative platform for green plant genomics [DOI]
- 6 Software for Computing and Annotating Genomic Ranges [DOI]
- 7 ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide [DOI]
- 8 Genome-Wide Mapping of in Vivo Protein-DNA Interactions [DOI]
- 9 Genome-wide association studies of 14 agronomic traits in rice landraces [DOI]
- 10 The advantages and limitations of trait analysis with GWAS: a review [DOI]
- 11 Phenomics – technologies to relieve the phenotyping bottleneck [DOI]
- 12 Genomic Selection for Crop Improvement [DOI]
- 13 The genome of the cucumber, Cucumis sativus L. [DOI]
- 14 The genetics of quantitative traits: challenges and prospects [DOI]
- 15 Genomic selection in plant breeding: from theory to practice [DOI]
- 16 Evolution of crop species: genetics of domestication and diversification [DOI]
- 17 A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety [DOI]
- 18 Genome-wide association study of leaf architecture in the maize nested association mapping population [DOI]
- 19 A High-Throughput Arabidopsis Reverse Genetics System [DOI]
- 20 Sequencing technologies and genome sequencing [DOI]
- 21 Molecular Plant Breeding as the Foundation for 21st Century Crop Improvement [DOI]
- 22 The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality [DOI]
- 23 Natural Variations and Genome-Wide Association Studies in Crop Plants [DOI]
- 24 Genomic Selection in Wheat Breeding using Genotyping‐by‐Sequencing [DOI]
- 25 Assessing the performance of the Oxford Nanopore Technologies MinION [DOI]
- 26 A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING [DOI]
- 27 Bioinformatics challenges for genome-wide association studies [DOI]
- 28 Hi-C: A Method to Study the Three-dimensional Architecture of Genomes. [DOI]
- 29 Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana [DOI]
- 30 Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum [DOI]
- 31 MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments [DOI]
- 32 Global agricultural intensification during climate change: a role for genomics [DOI]
- 33 Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing [DOI]
- 34 Accessing complex crop genomes with next-generation sequencing [DOI]
- 35 Application of Genomic Tools in Plant Breeding [DOI]
- 36 PlantGDB: a resource for comparative plant genomics [DOI]
- 37 A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton [DOI]
- 38 Genomic Selection for Quantitative Adult Plant Stem Rust Resistance in Wheat [DOI]
- 39 Most significant genome regions involved in the control of earliness traits in bread wheat, as revealed by QTL meta-analysis [DOI]
- 40 Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement [DOI]
- 41 Soybean oil content QTL mapping and integrating with meta-analysis method for mining genes [DOI]
- 42 Understanding and utilizing crop genome diversity via high‐resolution genotyping [DOI]
- 43 Genome-wide selection in cassava [DOI]
- 44 Prediction of adverse cardiac events in emergency department patients with chest pain using machine learning for variable selection [DOI]
- 45 The Impact of Genomics on the Study of Natural Variation in Arabidopsis [DOI]
- 46 One hundred important questions facing plant science research [DOI]
- 47 GrainGenes, the genome database for small-grain crops [DOI]
- 48 Genomic Databases for Crop Improvement [DOI]
- 49 Mining of Candidate Maize Genes for Nitrogen Use Efficiency by Integrating Gene Expression and QTL Data [DOI]
- 50 solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database [DOI]
- 51 PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses [DOI]
- 52 Coming of age: ten years of next-generation sequencing technologies [DOI]
- 53 The map-based sequence of the rice genome [DOI]
- 54 GAPIT: genome association and prediction integrated tool [DOI]
- 55 Nanopore sequencing and assembly of a human genome with ultra-long reads [DOI]
- 56 A chromosome conformation capture ordered sequence of the barley genome [DOI]
- 57 Speed breeding is a powerful tool to accelerate crop research and breeding [DOI]
- 58 Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing [DOI]
- 59 Piercing the dark matter: bioinformatics of long-range sequencing and mapping [DOI]
- 60 A survey of tools for variant analysis of next-generation genome sequencing data [DOI]
- 61 Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding [DOI]
- 62 Long-read sequence assembly of the gorilla genome [DOI]
- 63 The EMBL Nucleotide Sequence Database [DOI]
- 64 Systematic comparison of variant calling pipelines using gold standard personal exome variants [DOI]
- 65 High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell [DOI]
- 66 Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application [DOI]
- 67 Genome-wide Targeted Mutagenesis in Rice Using the CRISPR/Cas9 System [DOI]
- 68 Fine-mapping cellular QTLs with RASQUAL and ATAC-seq [DOI]
- 69 Construction of a Genome-Wide Mutant Library in Rice Using CRISPR/Cas9 [DOI]
- 70 The impact of third generation genomic technologies on plant genome assembly [DOI]
- 71 Gramene 2018: unifying comparative genomics and pathway resources for plant research [DOI]
- 72 Hi-C: A Method to Study the Three-dimensional Architecture of Genomes. [DOI]
- 73 BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes [DOI]
- 74 Adapting legume crops to climate change using genomic approaches [DOI]
- 75 Genome Sequencing and Assembly by Long Reads in Plants [DOI]
- 76 Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches [DOI]
- 77 Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes [DOI]
- 78 Genetic Gain and Inbreeding from Genomic Selection in a Simulated Commercial Breeding Program for Perennial Ryegrass [DOI]
- 79 The application of genomics and bioinformatics to accelerate crop improvement in a changing climate [DOI]
- 80 Genome-Wide Association Study of Genetic Control of Seed Fatty Acid Biosynthesis in Brassica napus [DOI]
- 81 Developing integrated crop knowledge networks to advance candidate gene discovery [DOI]
- 82 Application of next-generation sequencing in plant breeding [DOI]
- 83 Forward and Reverse Genetics in Crop Breeding [DOI]
- 84 Bioinformatics Approach in Plant Genomic Research [DOI]
- 85 Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes [DOI]
- 86 Lessons from Domestication: Targeting Cis-Regulatory Elements for Crop Improvement [DOI]
- 87 Revolution in Genotyping Platforms for Crop Improvement [DOI]
- 88 Addition of a breeding database in the Genome Database for Rosaceae [DOI]
- 89 The performance of activated sludge exposed to arsanilic acid and amprolium hydrochloride in sequencing batch reactors [DOI]
- 90 Databases for Wheat Genomics and Crop Improvement [DOI]
- 91 Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome [DOI]
- 92 Nanopore sequencing and assembly of a human genome with ultra-long reads [DOI]
- 93 Fine-mapping cellular QTLs with RASQUAL and ATAC-seq [DOI]
- 94 Integrating GIScience and Crop Science datasets: a study involving genetic, geographic and environmental data [DOI]
Cited by 14
Meghdad Kamali Moghaddam, Eman H. Afifi, Khaled F. M. Salem · Advances in Plant Breeding Strategies · 2025
Nimra Riasat, Amara Sana, Muhammad Hassaan Khan · Journal of Soil, Plant and Environment · 2024
Kempanna Sushmitha, Ganesan Megha, Monisha Domesa · CABI Biotechnology Series · 2026
Chayma Ikan, Fatima-Ezzahra Soussani, Redouane Ouhaddou · Plant Pangenomes and Pangenomics · 2025
Vinícius de Souza, Isaac Farias Cansanção, Edineia Bonin · 3 Biotech · 2026
Showing 5 of 14 known citations — external sources report more than can currently be individually listed.
Related research
- Development of a New Bifunctional Fusion Protein of Vaccine Strains Clostridium perfringens Type D and Clostridium septicum Epsilon-alpha Toxin Genes — shares topic coverage
- Host Plant Resistance to Important Viruses in Cucurbits- Current Challenges and Advances — shares topic coverage
- Pivotal Role of High Sensitivity Variant Calls and Confirmation Methods for Next-Generation Sequencing Findings: A Case Report — shares topic coverage
- A Review on Integrating Bioinformatics Tools in Modern Plant Breeding — shares topic coverage
- Analyses of Trypanosoma brucei Phospholipase A2 Structure and Function Using Bioinformatics Approach — shares topic coverage
Article metrics
Real usage data collected on this platform.
48
Page views
0
PDF downloads
5
Outbound clicks
14
Citations
Views over time
Views by country
Approximate, from request IP at view time — not citizenship or institution. Countries with fewer than 5 views are grouped as "Other".
Traffic sources
Referring site, by host.
Views and downloads exclude known bots/crawlers. Citations combines this platform's own DOI-resolved index with each external source's own reported total — see Cited by above for individually listed citing works. Last refreshed 0 seconds ago.